Ribotaper issue with container

[mkatsanto]

Hi, I have an issue with the ribotaper container https://quay.io/repository/biocontainers/ribotaper?tab=tags . None of the versions work, while the corresponding conda package works. There seems
to be an issue with the readlink version (see below for the detailed error). Can someone have a look?
Error

Usage: readlink [-fnv] FILE

Display the value of a symlink

    -f      Canonicalize by following all symlinks
    -n      Don't add newline
    -v      Verbose

readlink: invalid option -- 'e'
BusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.

Usage: readlink [-fnv] FILE

Display the value of a symlink

    -f      Canonicalize by following all symlinks
    -n      Don't add newline
    -v      Verbose

Parameters used:

<gtf_file>
<genome_fasta_file(indexed)>

[corneliusroemer]

Thanks for opening the issue!

Could you possibly provide the exact command(s) you run that result in output that's not how it should be?

How do you start the container, what did you run inside it? etc

It looks like you're trying to test for a symbolic link for a file that is not present in your container? Maybe you didn't mount the volume?

[mkatsanto]

Thanks for the reply, I am working on a linux system and the command failing is:

singularity exec ribotaper_1.3.1a--3.sif create_annotations_files.bash      \
   results/mus_musculus/gtf.wihout_scaffolds.gtf     \
   results/mus_musculus/genome.wihout_scaffolds.fasta   \
   false            false             results/mus_musculus/RiboTaper

where the options are as suggested in the manual.
The error is that the final files are empty.

In the case of conda which finished successfully, I activated the following env (in yaml):

---
channels:
  - conda-forge
  - bioconda
dependencies:
  - ribotaper=1.3.1
...

and then executed the same command :

create_annotations_files.bash             results/mus_musculus/gtf.wihout_scaffolds.gtf  \
     results/mus_musculus/genome.wihout_scaffolds.fasta             false            false  \
     results/mus_musculus/RiboTaper

I also executed the singularity command as part of a snakemake workflow and when I executed I made sure that the working directory was in the bindings. Also, other similar rules pointing to the same files and using singularity were executed. Do not know if this is helpful.

The line that seems to be failing in the code is here:
https://github.com/boboppie/RiboTaper/blob/2a8aa2efd131d29cb15dcf04a205e83de79d9b01/scripts/create_annotations_files.bash#L65

[corneliusroemer]

Ah great! It does indeed look like the version of readlink that the container uses (from busybox) does not support the option -e

Adding readlink as a run dependency might fix it, let's see if this works. Would be great if you could help test the output of that PR: #48937

[corneliusroemer]

@mkatsanto can you test with the latest container? It should be ready in a few minutes! Btw, hi across the street :p I see you're also in Basel :D Actually, same floor, how random to meet on bioconda-recipes.

[mkatsanto]

Yes will test and get back to you. Hello to you too. I just saw that as well. Haha that is random indeed.

[mkatsanto]

Is this the corrected version? 1.3.1a--h031d066_7
It is still not working.
An easy way to test is to do singularity run ribotaper_1.3.1a--h031d066_7.sif
and then run the readlink -e within the prompt.

[corneliusroemer]

Ah yeah sorry my bad, of course it doesn't work - I added "readline" not "readlink" 🤦 New PR: #48946

[corneliusroemer]

@mkatsanto could you please try again? Now I actually added "readlink" via "coreutils" and not readline :D

[mkatsanto]

Sorry for the delayed answer. It is working now! Thanks! I will close the issue now.

[corneliusroemer]

Excellent! Thanks for reporting and sorry for me readline messup 😄